CS102A Perl for Biologists, Level 2
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Taught in the context of biological research, this course shows biologists how to use the scripting language Perl to automate certain tasks. It is a continuation of CS101A Perl for Biologists, Level 1 and covers advanced topics and projects.
- Day 1: Perl basics (a quick review):
- How to use Perl commands in scripts and functions
- Good programming practices
- Specials notes, shortcuts, basic commands you may have forgotten
- Case study: Automating BLAST
- Downloading sequences and formating them for querying using the “formatdb.exe” program
- Creating FASTA file with sequences on which to use BLAST
- Writing a program to call “blastall.exe”, finding the best hits
- Case study: Gene expression analysis
- Reading ~20000 gene scores in a text file corresponding to 8 samples, and a gene information file
- Performing thresholding and normalization for this data
- Calculating fold change, difference, t-statistics, p-value, confidence intervals, etc.
- Outputing the filtered results, sorted by lower confidence interval, and removing Affymetrix control genes
- Day 2: Creating and using modules, namespaces, packages. References and object-oriented programming
- Day 3: The Perl DBI and DBD for the MySQL DBMS. Using BioPerl for sequence analysis
- Day 4: Project: Microarray database with sequence information
- Use SantaLucia rules to calculate the delta-G value of all 25-mer Perfect Match (PM) probe sequences.
- Create tables in a database using Perl to accommodate the data.
- Day 5: Project discussions
If you are interested in an upcoming course, register using instructions below. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)
- Step 1
- If you haven't already done so, create an on-line account to access the educational section of our website. Please note that the registration for our educational system is separate from that of the main website; you will require another account.
- Step 2
- Register for the course by making a payment using either the on-line registration form (click on the name of the course where it appears in the list of upcoming courses; use this form only for PayPal payments and credit card payments via secured PayPal), or by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).
Please also check the course tuition rates and discounts.
Registration deadline: When full
Tuition & discounts
- Live instruction held on-line
- For-profit & government: $500 USD
- Non-profit & self-pay: $300 USD
- Live instruction held on-site
- For-profit & government: $600 USD
- Non-profit & self-pay: $400 USD
- On-demand instruction held on-line
- For-profit & government: $300 USD
- Non-profit & self-pay: $200 USD
Additional discounts are available as follows:
- Professional members: 20% discount
- Limited scholarships may also be available for those residing in low-income economies (please inquire).
The necessary software, lecture notes and exercises will be provided.
Live instruction held on-line
On-line/live courses use the WebEx on-line meeting system. Access information will be provided prior to the start of the course. Unless otherwise noted, each lecture begins at 16:00 GMT and runs for about an hour, depending on the topics covered.
For those who cannot attend the lectures at those times, the lectures will be recorded and placed on the course website as AVI video files each day, within one day. Students will also be able to communicate with the instructor and other students via the course forums. Lecture attendance is therefore not required.
Since this will be an interactive, hands-on workshop, all attendees will need a computer with a broadband Internet connection (1 Mbps or faster is strongly recommended for those watching the live lecture), a sound card with speakers, a modern Web browser, and Java. A microphone and webcam are not required but may be used.
This course is certified by the Bioinformatics Organization, Inc., the largest international affiliation in the field, and it will count as 3 "Continuing Scientific Education" (CSE) units (one unit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.
For any course type, if a student is not satisfied with the conduct or content of a course, they may request a full refund within the first two days of lecture. After two days but within a week, a 50% refund will be granted. After one week, a 100% credit toward another course will be granted. No refunds or credits apply beyond those stated here.
Please contact us for questions or additional information.